default=sys.stdout)
args = parser.parse_args()
# First get the lineage (and fail now if not found)
lineage = get_lineage(args.species, args.email)
if not lineage:
raise RuntimeError(
"Could not find lineage information on NCBI for species '%s'" %
args.species)
print('Found lineage: %s' % lineage)
# Prepare the bibliographic reference
ref = Reference()
if args.ref_pubmed_id:
ref.pubmed_id = args.ref_pubmed_id
if args.ref_consortium:
ref.consrtm = args.ref_consortium
if args.ref_authors:
ref.authors = args.ref_authors
if args.ref_title:
ref.title = args.ref_title
if args.ref_journal:
ref.journal = args.ref_journal
else:
now = datetime.datetime.now()
ref_date = now.strftime("%m-%b-%Y").upper()
# Temp switch to C to get english month abbr
saved = locale.setlocale(locale.LC_TIME)
try:
locale.setlocale(locale.LC_TIME, "C")
print(gb, f)
# sort features by start location, source always first
gb.features.sort(key=lambda f: (-len(gb.seq)) *
(f.type == "source") + f.location.start)
# translate color from notes to ApEinfo
for feature in gb.features:
translate_color(feature)
# Add an EcoFlex article reference
ref = Reference()
ref.authors = 'Moore SJ, Lai HE, Kelwick RJ, Chee SM, Bell DJ, Polizzi KM, Freemont PS.'
ref.title = 'EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology.'
ref.journal = 'ACS Synth Biol 2016;5:1059-1069.'
ref.pubmed_id = '27096716'
gb.annotations['references'].append(ref)
# Fix the direct submission reference
ref = Reference()
# ref = gb.annotations["references"][-1]
ref.authors = "Larralde M"
ref.title = "Direct Submission"
ref.journal = "Distributed with the MoClo Python library\nhttps://github.com/althonos/moclo"
gb.annotations['references'].append(ref)
# write the final record
dst_dir = os.path.abspath(
os.path.join(__file__, "..", "..", "moclo-ecoflex", "registry",
"ecoflex"))
dst_file = os.path.join(dst_dir, "{}.gb").format(info["id"])
